Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing.

Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)-DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.

Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities.

Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R2 = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.

Single-Dose Rifapentine in Household Contacts of Patients with Leprosy.

BACKGROUND: Previous studies have suggested that a single dose of rifampin has protective effects against leprosy in close contacts of patients with the disease. Rifapentine was shown to have greater bactericidal activity against Mycobacterium leprae than rifampin in murine models of leprosy, but data regarding its effectiveness in preventing leprosy are lacking. METHODS: We conducted a cluster-randomized, controlled trial to investigate whether single-dose rifapentine is effective in preventing leprosy in household contacts of patients with leprosy. The clusters (counties or districts in Southwest China) were assigned to one of three trial groups: single-dose rifapentine, single-dose rifampin, or control (no intervention). The primary outcome was the 4-year cumulative incidence of leprosy among household contacts. RESULTS: A total of 207 clusters comprising 7450 household contacts underwent randomization; 68 clusters (2331 household contacts) were assigned to the rifapentine group, 71 (2760) to the rifampin group, and 68 (2359) to the control group. A total of 24 new cases of leprosy occurred over the 4-year follow-up, for a cumulative incidence of 0.09% (95% confidence interval [CI], 0.02 to 0.34) with rifapentine (2 cases), 0.33% (95% CI, 0.17 to 0.63) with rifampin (9 cases), and 0.55% (95% CI, 0.32 to 0.95) with no intervention (13 cases). In an intention-to-treat analysis, the cumulative incidence in the rifapentine group was 84% lower than that in the control group (cumulative incidence ratio, 0.16; multiplicity-adjusted 95% CI, 0.03 to 0.87; P = 0.02); the cumulative incidence did not differ significantly between the rifampin group and the control group (cumulative incidence ratio, 0.59; multiplicity-adjusted 95% CI, 0.22 to 1.57; P = 0.23). In a per-protocol analysis, the cumulative incidence was 0.05% with rifapentine, 0.19% with rifampin, and 0.63% with no intervention. No severe adverse events were observed. CONCLUSIONS: The incidence of leprosy among household contacts over 4 years was lower with single-dose rifapentine than with no intervention. (Funded by the Ministry of Health of China and the Chinese Academy of Medical Sciences; Chinese Clinical Trial Registry number, ChiCTR-IPR-15007075.).

Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats.

Due to the massive quantity and broad phylogeny, an accurate measurement of microbial diversity is highly challenging in soil ecosystems. Initially, the deviation caused by sampling should be adequately considered. Here, we attempted to uncover the effect of different sampling strategies on α diversity measurement of soil prokaryotes. Four 1 m2 sampling quadrats in a typical grassland were thoroughly surveyed through deep 16S rRNA gene sequencing (over 11 million reads per quadrat) with numerous replicates (33 soil sampling cores with total 141 replicates per quadrat). We found the difference in diversity was relatively small when pooling soil cores before and after DNA extraction and sequencing, but they were both superior to a non-pooling strategy. Pooling a small number of soil cores (i.e., 5 or 9) combined with several technical replicates is sufficient to estimate diversities for soil prokaryotes, and there is great flexibility in pooling original samples or data at different experimental steps. Additionally, the distribution of local α diversity varies with sampling core number, sequencing depth, and abundance distribution of the community, especially for high orders of Hill diversity index (i.e., Shannon entropy and inverse Simpson index). For each grassland soil quadrat (1 m2), retaining 100,000 reads after taxonomic clustering might be a realistic option, as these number of reads can efficiently cover the majority of common species in this area. Our findings provide important guidance for soil sampling strategy, and the general results can serve as a basis for further studies.

Preoperative vascular heterogeneity and aggressiveness assessment of pituitary macroadenoma based on dynamic contrast-enhanced MRI texture analysis.

PURPOSE: To assess the vascular heterogeneity and aggressiveness of pituitary macroadenomas (PM) using texture analysis based on Dynamic Contrast-Enhanced MRI (DCE-MRI). METHOD: Fifty patients with pathologically confirmed PM, including 32 patients with aggressive PM (aggressive group) and 18 patients with non-aggressive PM (non-aggressive group), were included in this study. The preoperative DCE-MRI and clinical data were collected from all patients. The features based on Ktrans, Ve, and Kep were generated using Omni-Kinetics software. Independent-samples t-test and Mann-Whitney U test were used for comparison between two groups. Logistic regression analysis was used to determine the optimal model for distinguishing aggressive and non-aggressive PM. RESULTS: Six features related to tumor morphology, 24 features in Ktrans, 20 features in Ve, and 3 features in Kep were significantly different between the aggressive and non-aggressive groups. Volume count, gray-level non-uniformity in Ktrans, voxel value sum in Ve and run-length non-uniformity in Kep (AUC = 0.816, 0.903, 0.785, 0.813) were considered the best feature for tumor diagnosis. After modeling, the diagnosis efficiency of mean model and total model was desirable (AUC = 0.859 and 0.957), and the diagnostic efficiency of morphological, Ktrans, Ve and Kep features model was improved (AUC = 0.845, 0.951, 0.847, 0.804). CONCLUSIONS: Texture analysis based on DCE-MRI elucidates the vascular heterogeneity and aggressiveness of pituitary adenoma. The total model could be used as a new noninvasive method for predicting the aggressiveness of pituitary macroadenoma.

Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved.

The gut microbime plays an important role in the health of wild animals. This microbial community could be altered by habitat pollution and other human activities that threaten the host organisms. Here, we satellite-tracked a flock of swan geese (Anser cygnoides) migrating from their breeding area (Khukh Lake, Mongolia), with low levels of human activity, to their wintering area (Poyang Lake, China) which has been heavily impacted by human activities. Twenty fecal samples were collected from each site. High-throughput sequencing of 16S and ITS was employed to explore bacterial and fungal composition and diversity of their gut microbiome. Although general composition, alpha-diversity, functional prediction, and the central taxa in the phylogenetic networks showed some similarities between the two habitats, significant divergences were detected in terms of beta-diversity, species abundances, and interaction network topologies. In addition, disease-related and xenobiotic biodegradation pathways, and pathogenic bacteria were significantly increased in bacterial communities from samples at Poyang Lake. Our results reveal that the gut microbiome of swan geese, while somewhat altered after long-distance migration, still maintained a core group of species. We also show that habitat environmental stress could impact these gut microbial communities, suggesting that habitat pollution could indirectly threaten wild animals by altering their gut microbiome.

The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants.

In this study, quantitative PCR (qPCR) and high-throughput sequencing were used to simultaneously examine both bacteria and fungi across temporal and spatial scales in activated sludge from wastewater treatment plants (WWTPs). The ratio of fungi to bacteria was 0.43% on average after accounting for the multicopies in 16S rRNA gene (54.63%), indicating the number of fungi was far lower than bacteria in active sludge. The Miseq sequencing results revealed obvious seasonal and spatial variations in bacterial and fungal distribution patterns in WWTPs. Compared to bacteria, fungi showed a lower divergence in alpha and beta diversity, and exhibited less taxonomic diversity in both abundant and rare subcommunities at the class level, suggesting that the fungal community was less variable in this artificial ecosystem. Such variation of microbial communities was significantly correlated with geographical distance, DO, temperature, HRT, SRT, COD, TN and TP. In activated sludge, the main function of bacteria was chemoheterotrophy, fermentation, and nitrogen cycling processes, while the dominant functional guilds of fungi were saprotroph, animal pathogen, and animal endosymbiont. Moreover, both bacteria and fungi could play important roles in the degradation of toxicants, like hydrocarbon and aromatic compounds.

A study on gender differences in newly detected leprosy cases in Sichuan, China, 2000-2015.

BACKGROUND: Many researches on gender differences in leprosy found that female patients were detected with the disease later and had more serious disabilities than male patients. We analyzed the gender differences related to epidemiological characteristics of new leprosy cases detected from 2000 to 2015 in Sichuan Province, China. METHODS: A retrospective study was undertaken to analyze the gender differences with respect to age, delay in disease detection, the main modes of detection, and disability grade. The chi-squared test and t test were applied for the comparison using Epi Info 7.2 with a significance level of a = 0.05. The data were collected from the Leprosy Management Information System in China. RESULTS: A total of 2900 new leprosy cases were detected from 2000 to 2015, of whom 2075 (71.6%) were male and 825 (28.4%) were female with a gender ratio of 2.5. The gender ratio of patients aged 15-30 was significantly lower than that of patients aged 31-45 and 46-60. Male cases were older than female cases when they were detected. The proportion of Grade 2 Disability (G2D) among men (20.6%) was significantly higher than that among women (17.3%). The average period of delay in detection among male cases was similar with that among females cases. CONCLUSIONS: Gender-related differences existed among the leprosy cases detected from 2000 to 2015. Female patients were younger than male patients. The detection of leprosy in women was not later than in the case of men. The disability situation in men was more serious than in women.

Association between genetic variants in NOD2, C13orf31, and CCDC122 genes and leprosy among the Chinese Yi population.

BACKGROUND: A significant association between single nucleotide polymorphisms in NOD2, C13orf31, and CCDC122 genes and leprosy has been reported in a previous genome-wide association study of leprosy in the Chinese Han population. However, it remains unknown whether this association exists among the Chinese Yi population. The aim of this study was to investigate whether single nucleotide polymorphisms in NOD2, C13orf31, and CCDC122 genes are associated with leprosy among the Chinese Yi population in China. METHODS: We genotyped rs9302752, rs7194886, rs8057341, and rs3135499 in the NOD2 gene; rs3764147 and rs10507522 in the C13orf31 gene; and rs3088362 and rs9533634 in the CCDC122 gene in a Chinese Yi cohort comprised of 319 patients with leprosy and 355 ethnic-matched controls. The differences between the patients and healthy controls were analyzed using chi-squared analysis. RESULTS: Significant differences of rs3135499 in NOD2, rs3764147 and rs10507522 in C13orf31, and rs3088362 and rs9533634 in CCDC122 were observed between the patients and the healthy control groups in the cohort. The allelic P values and odd ratios were as follows: rs3135499, 1.0 × 10(-8) and 2.55; rs3764147, 1.7 × 10(-7) and 1.88; rs10507522, 1.16 × 10(-5) and 1.95; rs3088362, 8.2 × 10(-4) and 1.51; rs9533634, 5.34 × 10(-5) and 1.73. No significant differences were found in the distributions of rs9302752, rs7194886, and rs8057341 between the patients and healthy controls. CONCLUSIONS: We demonstrated that genetic variants in the NOD2, C13orf31, and CCDC122 genes are closely associated with leprosy among the Chinese Yi population, which implicates the pathogenic role of NOD2, C13orf31, and CCDC122 genes in a different ethnicity.